Prosecutors did not name the other four senior managers charged.
VW first admitted in September 2015 that it had used illegal software to cheat US emissions tests.
The devices, which allowed cars to perform better in test conditions than they did on the road, were installed on almost 600,000 vehicles sold in the US from 2009 though 2015 and millions more globally.
They came to light after a study of emissions by researchers at West Virginia University in the US.
The Dieselgate scandal sparked investigations in Germany and other countries.
To date, the emissions scandal has cost Volkswagen roughly €28 billion, ($31 billion).
Last month, the US Securities and Exchange Commission (SEC) sued VW and Martin Winterkorn, accusing the company of “massive fraud” over the emissions scandal.
The SEC claims VW misled investors by issuing billions of dollars worth of bonds and securities, without disclosing that it had cheated emissions tests.
VW said it would contest the SEC lawsuit vigorously.
Porsche ex-CEO Wendelin Wiedeking and ex-finance chief Holger Haerter have gone on trial in Germany accused of market manipulation over a failed Volkswagen takeover bid.
Wendelin Wiedeking and Holger Haerter are accused of having given “false information” to investors.
Defense lawyers for the former executives have described the accusations as “unfounded”.
The failed bid opened the door to Porsche’s takeover by Volkswagen.
Between March and October 2008, Porsche issued several public denials that it was planning to raise its stake in VW to 75% and take over the company.
However, prosecutors said it was actually in the process of building up its shares in VW.
When Porsche announced it was planning to acquire enough of VW’s stock to take it over, Volkwagen’s share price shot up, and investment funds which needed to buy VW stock to settle their trading positions found none was available.
Then Porsche’s takeover bid failed, and left the sports car maker with €10 billion of debt.
VW launched a takeover of Porsche in turn, initially acquiring 49.9% of the sports car maker in 2009, before announcing in August 2012 that it had completed the acquisition.
Volkswagen has apologized after US regulators found some of its cars disguised pollution levels.
VW CEO Martin Winterkorn said: “I personally am deeply sorry that we have broken the trust of our customers and the public.”
He has launched an investigation into the device that allowed VW cars to emit less during tests than they would while driving normally.
The German automaker’s shares were down 19% in Frankfurt by lunchtime.
Volkswagen was ordered to recall half a million cars on September 18.
The Environmental Protection Agency (EPA) found the “defeat device” in diesel cars including the Audi A3, VW Jetta, Beetle, Golf and Passat models.
In addition to paying for the recall, VW faces fines that could add up to billions of dollars. There may also be criminal charges for VW executives.
The EPA said that the fine for each vehicle that did not comply with federal clean air rules would be up to $37,500. With 482,000 cars sold since 2008 involved in the allegations, it means the fines could reach $18 billion.
That would be a considerable amount, even for the company that recently overtook Toyota to be the world’s top-selling vehicle maker in the first six months of the year. Its stock market value is about €66 billion ($75 billion).
The company has stopped selling the relevant diesel models in the US, where diesel cars account for about a quarter of sales.
It has ordered an external investigation, although it has not revealed who will be conducting it.
“We do not and will not tolerate violations of any kind of our internal rules or of the law,” Martin Winterkorn said.
The German government said on September 21 it would rely on the US authorities to assess whether VW had done anything wrong in Europe.
“We expect the car companies to pass on reliable information so that the Federal Motor Transport Authority, the responsible authority in this case, can investigate whether similar manipulations took place with the emissions systems in Germany and Europe,” a spokesman for the German environment ministry said.
The scandal comes five months after former chairman Ferdinand Piech left Volkswagen following disagreements with Martin Winterkorn.
The VW board is due to meet on September 25 to decide whether to renew the chief executive’s contract until 2018.
“This disaster is beyond all expectations,” Ferdinand Dudenhoeffer, head of the Center of Automotive Research at the University of Duisburg-Essen, said.
VW had been promoting its diesel cars in the US as being better for the environment.
The US law firm Hagens Berman is launching a class-action suit against VW on behalf of people who bought the relevant cars.
The models cited by Hagens Berman are the diesel versions in the US of:
Jetta (2009 – 2015)
Beetle (2009 – 2015)
Audi A3 (2009 – 2015)
Golf (2009 – 2015)
Passat (2014 – 2015)
“While Volkswagen tells consumers that its diesel cars meet California emissions standards, vehicle owners are duped into paying for vehicles that do not meet this standard and unknowingly pay more for quality they never receive,” Hagens Berman alleged.